Variant report

Variant	rs1512343
Chromosome Location	chr4:149250957-149250958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10033040	0.84[CHD][hapmap]
rs10034789	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10519959	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13108130	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1512337	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17024708	0.83[CHB][hapmap]
rs17484601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17484622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17484671	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17581815	0.83[CHB][hapmap];0.95[CHD][hapmap];0.81[ASN][1000 genomes]
rs17581975	0.83[CHB][hapmap]
rs28612659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843414	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4835136	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4835515	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56221684	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67632846	0.90[ASN][1000 genomes]
rs6849903	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs7658039	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7698302	0.83[CHB][hapmap]
rs7700126	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs907618	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs9992528	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027263	chr4:149127120-149320135	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537296	chr4:149127120-149320135	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1031815	chr4:149172485-149282928	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1028105	chr4:149199913-149284620	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv537297	chr4:149199913-149284620	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1016966	chr4:149209467-149341037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1019350	chr4:149232430-149282117	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1512343	DCLK2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149235000-149266800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:149244400-149257600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:149245000-149251200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr4:149245200-149251400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:149245400-149251200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr4:149245400-149251400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr4:149245400-149257200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:149247400-149252000	Weak transcription	Aorta	Aorta
9	chr4:149248400-149252800	Enhancers	Fetal Heart	heart
10	chr4:149249400-149251400	Weak transcription	Right Ventricle	heart
11	chr4:149249400-149252800	Weak transcription	Lung	lung
12	chr4:149249400-149261400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:149249400-149263200	Weak transcription	Right Atrium	heart
14	chr4:149249400-149271200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr4:149249600-149252000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:149249800-149251400	Weak transcription	Psoas Muscle	Psoas
17	chr4:149250000-149253800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr4:149250400-149251400	Weak transcription	Left Ventricle	heart

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